6FM3 | pdb_00006fm3

Deoxyguanylosuccinate synthase (DgsS) structure with ADP at 1.9 Angstrom resolution

PDB DOI: https://doi.org/10.2210/pdb6FM3/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Vibrio phage phiVC8
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2018-01-30 Released: 2019-06-12
Deposition Author(s): Sleiman, D., Loc'h, J., Haouz, A., Kaminski, P.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.252 (Depositor), 0.239 (DCC)
R-Value Work:
0.220 (Depositor), 0.225 (DCC)
R-Value Observed:
0.222 (Depositor)

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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Deoxyguanylosuccinate synthase (DgsS) quaternary structure with ATP0, dGMP, Magnesium at 2.3 Angstrom resolution

Sleiman, D., Loc'h, J., Haouz, A., Kaminski, P.A.

To be published.

Macromolecule Content

Total Structure Weight: 40.86 kDa
Atom Count: 2,742
Modeled Residue Count: 304
Deposited Residue Count: 363
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenylosuccinate synthetase	A	363	Vibrio phage phiVC8	Mutation(s): 0 Gene Names: phiVC8_p27 EC: 6.3.4.25
UniProt
Find proteins for G3FFN6 (Vibrio phage phiVC8) Explore G3FFN6 Go to UniProtKB: G3FFN6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G3FFN6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP (Subject of Investigation/LOI) Query on ADP Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.252 (Depositor), 0.239 (DCC)
R-Value Work: 0.220 (Depositor), 0.225 (DCC)
R-Value Observed: 0.222 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.78	α = 90
b = 58.2	β = 102.44
c = 71.96	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2019-06-12

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2019-06-12
Type: Initial release
Version 1.1: 2024-05-08
Changes: Data collection, Database references

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.